Fix get_map_data() and slicing for crystal maps whose coordinates do not start at zero

CHANGELOG.rst

@@ -43,6 +43,9 @@ Fixed
   multi-dimensional orientations.
 - Quaternions plotted in a 3D projection (axis-Angle, Rodrigues, homochoric, etc.) will
   now correctly be transformed using the same algorithms as for rotations.
+- ``CrystalMap.get_map_data()`` and slicing a crystal map now work for maps whose
+  coordinates do not start at zero. Previously, an empty array was returned or a
+  ``ValueError`` was raised.
 
 Deprecated
 ----------

orix/crystal_map/crystal_map.py

@@ -1089,11 +1089,19 @@ def _data_slices_from_coordinates(self, only_is_in_data: bool = True) -> tuple:
         slices
             Data slice in each existing direction in (y, x) order.
         """
+        steps = self._step_sizes
         if only_is_in_data:
             coordinates = self._coordinates
         else:
             coordinates = self._all_coordinates
-        slices = _data_slices_from_coordinates(coordinates, self._step_sizes)
+        slices = _data_slices_from_coordinates(coordinates, steps)
+        # Make slices relative to the first point in the full map, so
+        # that maps whose coordinates do not start at zero can be
+        # indexed into arrays of the original map shape
+        origin = _data_slices_from_coordinates(self._all_coordinates, steps)
+        slices = tuple(
+            slice(s.start - o.start, s.stop - o.start) for s, o in zip(slices, origin)
+        )
         return slices
 
     def _data_shape_from_coordinates(self, only_is_in_data: bool = True) -> tuple:

orix/tests/test_crystal_map/test_crystal_map.py

@@ -1140,6 +1140,22 @@ def test_coordinate_axes(self, crystal_map_input, expected_coordinate_axes):
         xmap = CrystalMap(**crystal_map_input)
         assert xmap._coordinate_axes == expected_coordinate_axes
 
+    def test_coordinates_not_starting_at_zero(self):
+        # E.g. a region of interest exported with stage coordinates
+        d, map_size = create_coordinate_arrays((3, 4), step_sizes=(0.5, 0.5))
+        d["x"] = d["x"] + 10
+        d["y"] = d["y"] + 3
+        xmap = CrystalMap(rotations=Rotation.identity(map_size), **d)
+        assert xmap.shape == (3, 4)
+        x = xmap.get_map_data("x")
+        assert x.shape == (3, 4)
+        assert np.allclose(x[0], [10, 10.5, 11, 11.5])
+
+        xmap2 = xmap[1:, 1:]
+        assert xmap2.shape == (2, 3)
+        assert np.allclose(xmap2.get_map_data("x")[0], [10.5, 11, 11.5])
+        assert np.allclose(xmap2.get_map_data("y")[:, 0], [3.5, 4])
+
     def test_data_slices_from_coordinates_no_steps(self):
         d, _ = create_coordinate_arrays((3, 4), step_sizes=(0.1, 0.2))
         slices = _data_slices_from_coordinates(d)